submit query to sierra

src/viewer/ui/strucmotif.tsx

@@ -20,6 +20,11 @@ import {StructureSelectionHistoryEntry} from 'molstar/lib/mol-plugin-state/manag
 import {StructureElement} from 'molstar/lib/mol-model/structure/structure';
 import {ToggleSelectionModeButton} from 'molstar/lib/mol-plugin-ui/structure/selection';
 
+// TODO use prod
+// const ADVANCED_SEARCH_URL = 'https://strucmotif-dev.rcsb.org/search?request=';
+const ADVANCED_SEARCH_URL = 'http://localhost:8080/search?request=';
+const MAX_MOTIF_SIZE = 10;
+
 export class StrucmotifSubmitControls extends CollapsableControls {
     protected defaultState() {
         return {
@@ -57,13 +62,72 @@ export class SubmitControls extends PurePluginUIComponent<{}, { isBusy: boolean
     }
 
     submitSearch = () => {
+        // TODO ensure selection is from single structure
+        // TODO ensure selection references only polymeric entities
+        // TODO ensure selection granularity is/was residue
+        const pdbId: Set<string> = new Set();
+        const residueIds = [
+            { label_asym_id: 'B', struct_oper_id: '1', label_seq_id: 42 },
+            { label_asym_id: 'B', struct_oper_id: '1', label_seq_id: 87 },
+            { label_asym_id: 'C', struct_oper_id: '1', label_seq_id: 47 }
+        ];
         const loci = this.plugin.managers.structure.selection.additionsHistory;
-        // this.plugin.managers.structure.measurement.addAngle(loci[0].loci, loci[1].loci, loci[2].loci);
-        console.log(loci[0].loci.elements);
-        window.open('https://rcsb.org', '_blank');
+        console.log(loci[0].loci.structure);
+        for (let l of loci) {
+            pdbId.add(l.loci.structure.model.entry);
+        }
+        if (pdbId.size > 1) {
+            console.warn('motifs can only be extracted from a single model');
+            return;
+        }
+        if (residueIds.length > MAX_MOTIF_SIZE) {
+            console.warn(`maximum motif size is ${MAX_MOTIF_SIZE} residues`);
+            return;
+        }
+        const query = {
+            'query': {
+                'type': 'group',
+                'logical_operator': 'and',
+                'nodes': [{
+                    'type': 'terminal',
+                    'service': 'strucmotif',
+                    'parameters': {
+                        'value': {
+                            'data': '4CHA'/* pdbId.values().next().value as string*/,
+                            'residue_ids': residueIds
+                        },
+                        'score_cutoff': 5,
+                        'exchanges': []
+                    },
+                    'label': 'strucmotif',
+                    'node_id': 0
+                }],
+                'label': 'query-builder'
+            },
+            'return_type': 'assembly',
+            'request_options': {
+                'pager': {
+                    'start': 0,
+                    'rows': 100
+                },
+                'scoring_strategy': 'combined',
+                'sort': [{
+                    'sort_by': 'score',
+                    'direction': 'desc'
+                }]
+            },
+            // TODO needed?
+            // 'request_info': {
+            // 'src': 'ui',
+            // 'query_id': 'a4efda380aee3ef202dc59447a419e80'
+            // }
+        };
+        // TODO figure out of Mol* can compose sierra/BioJava operator
+        // TODO probably there should be a sierra-endpoint that handles mapping of Mol* operator ids to sierra/BioJava ones
+        console.log(encodeURIComponent(JSON.stringify(query)).replace('%22', '"'));
+        window.open(ADVANCED_SEARCH_URL + encodeURIComponent(JSON.stringify(query)), '_blank');
     }
 
-
     get actions(): ActionMenu.Items {
         const history = this.selection.additionsHistory;
         const ret: ActionMenu.Item[] = [